Voltage-gated ion channels in nerve cells that open and close in response to binding of its specific ligand (such as a neurotransmitter) or by a change in the transmembrane electric potential.

Molecular dynamics

Molecular dynamics simulates the macroscopic behaviour of a microscopic many-body system through the numerical integration of Newton’s equations of motion. It is a powerful computational method that allows us to follow and understand structure and dynamics in extreme detail, on a scale where the trajectories of individual atoms can be tracked. The macroscopic properties of the whole simulation system are expressed as functions of particle coordinates and momenta, which are computed along a trajectory generated by classical dynamics.

The time evolution of the system are driven by forces between particles, which in turn derive from a potential energy function V, also called the force field. The function V defines the interaction terms between pairs of atoms and is typically divided into “bonded” and “non-bonded” interactions. The bonded interactions consist of bond stretching (Ebond), angle bending (Eangle) and dihedral angle deformation (Etorsion). Non-bonded interactions include electrostatic (Eelec) and van der Waals terms (Evdw). A set of atomic positions and velocities are then generated as a function of time, which evolve deterministically from an initial configuration according to the force field V.